## Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
##   object 'config' not found

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: Viral read count

Canonic Transcript dynamics (TSS ~ TES)

Those reads were counted only, where both the 3-prime AND the 5-prime adapters were “correct” (according to LoRTIA)

When counting with either adapters, the clustering grouped ORF64 together with two late genes

Statistics of counts

Difference from mean

Varcoeff

Clustering of samples

## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.7)... Done.
## Bootstrap (r = 0.79)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.2)... Done.
## Bootstrap (r = 1.29)... Done.
## Bootstrap (r = 1.39)... Done.

The sample 48h_3 stands out!

Filtering of samples

Clustering of genes into de-novo clusters using hierarchial clustering

Cluster memberships

## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.58)... Done.
## Bootstrap (r = 0.69)... Done.
## Bootstrap (r = 0.77)... Done.
## Bootstrap (r = 0.88)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.08)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.27)... Done.
## Bootstrap (r = 1.38)... Done.

Optimal number of clusters

Find the optimal number of clusters to cut the tree at and calculate

Clustering statistics: Cluster number: 5

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  2:       1    ORF2 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  3:       1    ORF3 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  4:       1    ORF4 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  5:       1    ORF8 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  6:       1    ORF9 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  7:       1   ORF11 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  8:       1   ORF14 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  9:       1   ORF18 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 10:       1   ORF19 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 11:       1   ORF20 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 12:       1   ORF21 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 13:       1   ORF22 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 14:       1   ORF23 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 15:       1   ORF24 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 16:       1   ORF25 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 17:       1   ORF26 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 18:       1   ORF28 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 19:       1   ORF29 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 20:       1   ORF31 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 21:       1   ORF33 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 22:       1   ORF34 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 23:       1 ORF35.5 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 24:       1   ORF36 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 25:       1   ORF37 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 26:       1   ORF38 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 27:       1   ORF39 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 28:       1     CTO 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 29:       1   ORF40 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 30:       1   ORF42 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 31:       1   ORF43 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 32:       1   ORF44 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 33:       1   ORF46 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 34:       1   ORF49 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 35:       1   ORF50 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 36:       1   ORF51 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 37:       1   ORF58 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 38:       1   ORF61 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 39:       1   ORF62 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 40:       1 ORF64_1 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 41:       1 ORF66_1 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 42:       1   ORF68 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 43:       1   ORF73 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 44:       1   ORF74 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 45:       1   ORF75 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 46:       1   ORF76 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 47:       2    ORF5 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 48:       2    ORF7 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 49:       2   ORF10 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 50:       2   ORF17 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 51:       2   ORF30 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 52:       2   ORF53 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 53:       2   ORF63 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 54:       2  NOIR_2 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 55:       3    ORF6 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 56:       3 ORF65_1 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 57:       3 ORF67_1 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 58:       4   ORF12 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 59:       4   ORF13 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 60:       4   ORF15 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 61:       4   ORF16 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 62:       4   ORF27 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 63:       4   ORF32 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 64:       4   ORF35 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 65:       4   ORF41 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 66:       4   ORF48 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 67:       4   ORF52 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 68:       4   ORF54 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 69:       4   ORF57 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 70:       4   ORF59 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 71:       4   ORF60 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 72:       4  NOIR_1 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 73:       4   ORF71 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 74:       4   ORF72 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 75:       5   ORF69 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 76:       5   ORF70 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.002430598 -2.7030290 0.9688488 0.39059013
##  2: 0.002430598 -2.7030290 0.9688488 0.39059013
##  3: 0.002430598 -2.7030290 0.9688488 0.39059013
##  4: 0.002430598 -2.7030290 0.9688488 0.39059013
##  5: 0.002430598 -2.7030290 0.9688488 0.39059013
##  6: 0.002430598 -2.7030290 0.9688488 0.39059013
##  7: 0.002430598 -2.7030290 0.9688488 0.39059013
##  8: 0.002430598 -2.7030290 0.9688488 0.39059013
##  9: 0.002430598 -2.7030290 0.9688488 0.39059013
## 10: 0.002430598 -2.7030290 0.9688488 0.39059013
## 11: 0.002430598 -2.7030290 0.9688488 0.39059013
## 12: 0.002430598 -2.7030290 0.9688488 0.39059013
## 13: 0.002430598 -2.7030290 0.9688488 0.39059013
## 14: 0.002430598 -2.7030290 0.9688488 0.39059013
## 15: 0.002430598 -2.7030290 0.9688488 0.39059013
## 16: 0.002430598 -2.7030290 0.9688488 0.39059013
## 17: 0.002430598 -2.7030290 0.9688488 0.39059013
## 18: 0.002430598 -2.7030290 0.9688488 0.39059013
## 19: 0.002430598 -2.7030290 0.9688488 0.39059013
## 20: 0.002430598 -2.7030290 0.9688488 0.39059013
## 21: 0.002430598 -2.7030290 0.9688488 0.39059013
## 22: 0.002430598 -2.7030290 0.9688488 0.39059013
## 23: 0.002430598 -2.7030290 0.9688488 0.39059013
## 24: 0.002430598 -2.7030290 0.9688488 0.39059013
## 25: 0.002430598 -2.7030290 0.9688488 0.39059013
## 26: 0.002430598 -2.7030290 0.9688488 0.39059013
## 27: 0.002430598 -2.7030290 0.9688488 0.39059013
## 28: 0.002430598 -2.7030290 0.9688488 0.39059013
## 29: 0.002430598 -2.7030290 0.9688488 0.39059013
## 30: 0.002430598 -2.7030290 0.9688488 0.39059013
## 31: 0.002430598 -2.7030290 0.9688488 0.39059013
## 32: 0.002430598 -2.7030290 0.9688488 0.39059013
## 33: 0.002430598 -2.7030290 0.9688488 0.39059013
## 34: 0.002430598 -2.7030290 0.9688488 0.39059013
## 35: 0.002430598 -2.7030290 0.9688488 0.39059013
## 36: 0.002430598 -2.7030290 0.9688488 0.39059013
## 37: 0.002430598 -2.7030290 0.9688488 0.39059013
## 38: 0.002430598 -2.7030290 0.9688488 0.39059013
## 39: 0.002430598 -2.7030290 0.9688488 0.39059013
## 40: 0.002430598 -2.7030290 0.9688488 0.39059013
## 41: 0.002430598 -2.7030290 0.9688488 0.39059013
## 42: 0.002430598 -2.7030290 0.9688488 0.39059013
## 43: 0.002430598 -2.7030290 0.9688488 0.39059013
## 44: 0.002430598 -2.7030290 0.9688488 0.39059013
## 45: 0.002430598 -2.7030290 0.9688488 0.39059013
## 46: 0.002430598 -2.7030290 0.9688488 0.39059013
## 47: 0.004779760 -1.4851268 0.8321862 0.03126641
## 48: 0.004779760 -1.4851268 0.8321862 0.03126641
## 49: 0.004779760 -1.4851268 0.8321862 0.03126641
## 50: 0.004779760 -1.4851268 0.8321862 0.03126641
## 51: 0.004779760 -1.4851268 0.8321862 0.03126641
## 52: 0.004779760 -1.4851268 0.8321862 0.03126641
## 53: 0.004779760 -1.4851268 0.8321862 0.03126641
## 54: 0.004779760 -1.4851268 0.8321862 0.03126641
## 55: 0.003860428 -2.3311288 1.1560091 0.25094155
## 56: 0.003860428 -2.3311288 1.1560091 0.25094155
## 57: 0.003860428 -2.3311288 1.1560091 0.25094155
## 58: 0.004540032 -1.5343905 0.7544213 0.01116250
## 59: 0.004540032 -1.5343905 0.7544213 0.01116250
## 60: 0.004540032 -1.5343905 0.7544213 0.01116250
## 61: 0.004540032 -1.5343905 0.7544213 0.01116250
## 62: 0.004540032 -1.5343905 0.7544213 0.01116250
## 63: 0.004540032 -1.5343905 0.7544213 0.01116250
## 64: 0.004540032 -1.5343905 0.7544213 0.01116250
## 65: 0.004540032 -1.5343905 0.7544213 0.01116250
## 66: 0.004540032 -1.5343905 0.7544213 0.01116250
## 67: 0.004540032 -1.5343905 0.7544213 0.01116250
## 68: 0.004540032 -1.5343905 0.7544213 0.01116250
## 69: 0.004540032 -1.5343905 0.7544213 0.01116250
## 70: 0.004540032 -1.5343905 0.7544213 0.01116250
## 71: 0.004540032 -1.5343905 0.7544213 0.01116250
## 72: 0.004540032 -1.5343905 0.7544213 0.01116250
## 73: 0.004540032 -1.5343905 0.7544213 0.01116250
## 74: 0.004540032 -1.5343905 0.7544213 0.01116250
## 75: 0.005075046 -0.7430393 0.3591568 0.52357949
## 76: 0.005075046 -0.7430393 0.3591568 0.52357949
##           se.bp          v         c       pchi

##  [1] "ORF44"   "ORF58"   "ORF25"   "ORF35.5" "ORF64_1" "ORF50"   "ORF42"  
##  [8] "ORF33"   "ORF34"   "ORF62"   "ORF4"    "ORF20"   "ORF21"   "ORF61"  
## [15] "ORF31"   "ORF1"    "NOIR_1"  "ORF32"   "ORF59"   "ORF69"
## [1] 20
## [1] "ORF69" "ORF70"
## [1] 2

Clustering statistics: Cluster number: 6

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  2:       1    ORF4 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  3:       1    ORF9 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  4:       1   ORF19 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  5:       1   ORF20 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  6:       1   ORF21 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  7:       1   ORF31 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  8:       1   ORF34 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  9:       1   ORF37 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 10:       1   ORF38 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 11:       1   ORF49 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 12:       1   ORF50 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 13:       1   ORF51 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 14:       1   ORF61 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 15:       1 ORF64_1 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 16:       2    ORF2 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 17:       2    ORF3 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 18:       2    ORF8 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 19:       2   ORF11 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 20:       2   ORF14 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 21:       2   ORF18 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 22:       2   ORF22 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 23:       2   ORF23 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 24:       2   ORF24 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 25:       2   ORF25 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 26:       2   ORF26 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 27:       2   ORF28 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 28:       2   ORF29 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 29:       2   ORF33 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 30:       2 ORF35.5 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 31:       2   ORF36 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 32:       2   ORF39 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 33:       2     CTO 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 34:       2   ORF40 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 35:       2   ORF42 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 36:       2   ORF43 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 37:       2   ORF44 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 38:       2   ORF46 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 39:       2   ORF58 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 40:       2   ORF62 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 41:       2 ORF66_1 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 42:       2   ORF68 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 43:       2   ORF73 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 44:       2   ORF74 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 45:       2   ORF75 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 46:       2   ORF76 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 47:       3    ORF5 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 48:       3    ORF7 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 49:       3   ORF10 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 50:       3   ORF17 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 51:       3   ORF30 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 52:       3   ORF53 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 53:       3   ORF63 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 54:       3  NOIR_2 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 55:       4    ORF6 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 56:       4 ORF65_1 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 57:       4 ORF67_1 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 58:       5   ORF12 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 59:       5   ORF13 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 60:       5   ORF15 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 61:       5   ORF16 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 62:       5   ORF27 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 63:       5   ORF32 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 64:       5   ORF35 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 65:       5   ORF41 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 66:       5   ORF48 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 67:       5   ORF52 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 68:       5   ORF54 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 69:       5   ORF57 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 70:       5   ORF59 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 71:       5   ORF60 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 72:       5  NOIR_1 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 73:       5   ORF71 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 74:       5   ORF72 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 75:       6   ORF69 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 76:       6   ORF70 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.002430598 -2.7030290 0.9688488 0.39059013
##  2: 0.002430598 -2.7030290 0.9688488 0.39059013
##  3: 0.002430598 -2.7030290 0.9688488 0.39059013
##  4: 0.002430598 -2.7030290 0.9688488 0.39059013
##  5: 0.002430598 -2.7030290 0.9688488 0.39059013
##  6: 0.002430598 -2.7030290 0.9688488 0.39059013
##  7: 0.002430598 -2.7030290 0.9688488 0.39059013
##  8: 0.002430598 -2.7030290 0.9688488 0.39059013
##  9: 0.002430598 -2.7030290 0.9688488 0.39059013
## 10: 0.002430598 -2.7030290 0.9688488 0.39059013
## 11: 0.002430598 -2.7030290 0.9688488 0.39059013
## 12: 0.002430598 -2.7030290 0.9688488 0.39059013
## 13: 0.002430598 -2.7030290 0.9688488 0.39059013
## 14: 0.002430598 -2.7030290 0.9688488 0.39059013
## 15: 0.002430598 -2.7030290 0.9688488 0.39059013
## 16: 0.004779760 -1.4851268 0.8321862 0.03126641
## 17: 0.004779760 -1.4851268 0.8321862 0.03126641
## 18: 0.004779760 -1.4851268 0.8321862 0.03126641
## 19: 0.004779760 -1.4851268 0.8321862 0.03126641
## 20: 0.004779760 -1.4851268 0.8321862 0.03126641
## 21: 0.004779760 -1.4851268 0.8321862 0.03126641
## 22: 0.004779760 -1.4851268 0.8321862 0.03126641
## 23: 0.004779760 -1.4851268 0.8321862 0.03126641
## 24: 0.004779760 -1.4851268 0.8321862 0.03126641
## 25: 0.004779760 -1.4851268 0.8321862 0.03126641
## 26: 0.004779760 -1.4851268 0.8321862 0.03126641
## 27: 0.004779760 -1.4851268 0.8321862 0.03126641
## 28: 0.004779760 -1.4851268 0.8321862 0.03126641
## 29: 0.004779760 -1.4851268 0.8321862 0.03126641
## 30: 0.004779760 -1.4851268 0.8321862 0.03126641
## 31: 0.004779760 -1.4851268 0.8321862 0.03126641
## 32: 0.004779760 -1.4851268 0.8321862 0.03126641
## 33: 0.004779760 -1.4851268 0.8321862 0.03126641
## 34: 0.004779760 -1.4851268 0.8321862 0.03126641
## 35: 0.004779760 -1.4851268 0.8321862 0.03126641
## 36: 0.004779760 -1.4851268 0.8321862 0.03126641
## 37: 0.004779760 -1.4851268 0.8321862 0.03126641
## 38: 0.004779760 -1.4851268 0.8321862 0.03126641
## 39: 0.004779760 -1.4851268 0.8321862 0.03126641
## 40: 0.004779760 -1.4851268 0.8321862 0.03126641
## 41: 0.004779760 -1.4851268 0.8321862 0.03126641
## 42: 0.004779760 -1.4851268 0.8321862 0.03126641
## 43: 0.004779760 -1.4851268 0.8321862 0.03126641
## 44: 0.004779760 -1.4851268 0.8321862 0.03126641
## 45: 0.004779760 -1.4851268 0.8321862 0.03126641
## 46: 0.004779760 -1.4851268 0.8321862 0.03126641
## 47: 0.003860428 -2.3311288 1.1560091 0.25094155
## 48: 0.003860428 -2.3311288 1.1560091 0.25094155
## 49: 0.003860428 -2.3311288 1.1560091 0.25094155
## 50: 0.003860428 -2.3311288 1.1560091 0.25094155
## 51: 0.003860428 -2.3311288 1.1560091 0.25094155
## 52: 0.003860428 -2.3311288 1.1560091 0.25094155
## 53: 0.003860428 -2.3311288 1.1560091 0.25094155
## 54: 0.003860428 -2.3311288 1.1560091 0.25094155
## 55: 0.004540032 -1.5343905 0.7544213 0.01116250
## 56: 0.004540032 -1.5343905 0.7544213 0.01116250
## 57: 0.004540032 -1.5343905 0.7544213 0.01116250
## 58: 0.005075046 -0.7430393 0.3591568 0.52357949
## 59: 0.005075046 -0.7430393 0.3591568 0.52357949
## 60: 0.005075046 -0.7430393 0.3591568 0.52357949
## 61: 0.005075046 -0.7430393 0.3591568 0.52357949
## 62: 0.005075046 -0.7430393 0.3591568 0.52357949
## 63: 0.005075046 -0.7430393 0.3591568 0.52357949
## 64: 0.005075046 -0.7430393 0.3591568 0.52357949
## 65: 0.005075046 -0.7430393 0.3591568 0.52357949
## 66: 0.005075046 -0.7430393 0.3591568 0.52357949
## 67: 0.005075046 -0.7430393 0.3591568 0.52357949
## 68: 0.005075046 -0.7430393 0.3591568 0.52357949
## 69: 0.005075046 -0.7430393 0.3591568 0.52357949
## 70: 0.005075046 -0.7430393 0.3591568 0.52357949
## 71: 0.005075046 -0.7430393 0.3591568 0.52357949
## 72: 0.005075046 -0.7430393 0.3591568 0.52357949
## 73: 0.005075046 -0.7430393 0.3591568 0.52357949
## 74: 0.005075046 -0.7430393 0.3591568 0.52357949
## 75: 0.005372412 -1.2236534 1.2270317 0.25941579
## 76: 0.005372412 -1.2236534 1.2270317 0.25941579
##           se.bp          v         c       pchi

##  [1] "ORF61"  "ORF21"  "ORF49"  "ORF19"  "ORF31"  "ORF1"   "ORF62"  "ORF18" 
##  [9] "ORF32"  "ORF59"  "NOIR_1" "ORF69"
## [1] 12
##  [1] "ORF12"  "ORF13"  "ORF15"  "ORF16"  "ORF27"  "ORF32"  "ORF35"  "ORF41" 
##  [9] "ORF48"  "ORF52"  "ORF54"  "ORF57"  "ORF59"  "ORF60"  "NOIR_1" "ORF71" 
## [17] "ORF72"
## [1] 17

Clustering statistics: Cluster number: 7

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  2:       1    ORF4 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  3:       1    ORF9 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  4:       1   ORF19 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  5:       1   ORF20 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  6:       1   ORF21 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  7:       1   ORF31 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  8:       1   ORF34 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  9:       1   ORF37 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 10:       1   ORF38 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 11:       1   ORF49 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 12:       1   ORF50 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 13:       1   ORF51 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 14:       1   ORF61 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 15:       1 ORF64_1 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 16:       2    ORF2 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 17:       2    ORF3 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 18:       2    ORF8 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 19:       2   ORF11 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 20:       2   ORF14 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 21:       2   ORF18 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 22:       2   ORF22 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 23:       2   ORF23 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 24:       2   ORF24 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 25:       2   ORF25 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 26:       2   ORF26 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 27:       2   ORF28 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 28:       2   ORF29 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 29:       2   ORF33 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 30:       2 ORF35.5 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 31:       2   ORF36 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 32:       2   ORF39 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 33:       2     CTO 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 34:       2   ORF40 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 35:       2   ORF42 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 36:       2   ORF43 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 37:       2   ORF44 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 38:       2   ORF46 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 39:       2   ORF58 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 40:       2   ORF62 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 41:       2 ORF66_1 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 42:       2   ORF68 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 43:       2   ORF73 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 44:       2   ORF74 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 45:       2   ORF75 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 46:       2   ORF76 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 47:       3    ORF5 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 48:       3    ORF7 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 49:       3   ORF10 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 50:       3   ORF17 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 51:       3   ORF30 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 52:       3   ORF53 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 53:       3   ORF63 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 54:       3  NOIR_2 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 55:       4    ORF6 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 56:       4 ORF65_1 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 57:       4 ORF67_1 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 58:       5   ORF12 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 59:       5   ORF13 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 60:       5   ORF15 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 61:       5   ORF16 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 62:       5   ORF35 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 63:       5   ORF41 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 64:       5   ORF48 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 65:       5   ORF52 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 66:       5   ORF54 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 67:       5   ORF57 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 68:       5   ORF60 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 69:       5   ORF71 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 70:       5   ORF72 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 71:       6   ORF27 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 72:       6   ORF32 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 73:       6   ORF59 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 74:       6  NOIR_1 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 75:       7   ORF69 0.9943260 0.9992519 0.8263791 0.0013907764 2.320885e-04
## 76:       7   ORF70 0.9943260 0.9992519 0.8263791 0.0013907764 2.320885e-04
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.002430598 -2.7030290 0.9688488 0.39059013
##  2: 0.002430598 -2.7030290 0.9688488 0.39059013
##  3: 0.002430598 -2.7030290 0.9688488 0.39059013
##  4: 0.002430598 -2.7030290 0.9688488 0.39059013
##  5: 0.002430598 -2.7030290 0.9688488 0.39059013
##  6: 0.002430598 -2.7030290 0.9688488 0.39059013
##  7: 0.002430598 -2.7030290 0.9688488 0.39059013
##  8: 0.002430598 -2.7030290 0.9688488 0.39059013
##  9: 0.002430598 -2.7030290 0.9688488 0.39059013
## 10: 0.002430598 -2.7030290 0.9688488 0.39059013
## 11: 0.002430598 -2.7030290 0.9688488 0.39059013
## 12: 0.002430598 -2.7030290 0.9688488 0.39059013
## 13: 0.002430598 -2.7030290 0.9688488 0.39059013
## 14: 0.002430598 -2.7030290 0.9688488 0.39059013
## 15: 0.002430598 -2.7030290 0.9688488 0.39059013
## 16: 0.004779760 -1.4851268 0.8321862 0.03126641
## 17: 0.004779760 -1.4851268 0.8321862 0.03126641
## 18: 0.004779760 -1.4851268 0.8321862 0.03126641
## 19: 0.004779760 -1.4851268 0.8321862 0.03126641
## 20: 0.004779760 -1.4851268 0.8321862 0.03126641
## 21: 0.004779760 -1.4851268 0.8321862 0.03126641
## 22: 0.004779760 -1.4851268 0.8321862 0.03126641
## 23: 0.004779760 -1.4851268 0.8321862 0.03126641
## 24: 0.004779760 -1.4851268 0.8321862 0.03126641
## 25: 0.004779760 -1.4851268 0.8321862 0.03126641
## 26: 0.004779760 -1.4851268 0.8321862 0.03126641
## 27: 0.004779760 -1.4851268 0.8321862 0.03126641
## 28: 0.004779760 -1.4851268 0.8321862 0.03126641
## 29: 0.004779760 -1.4851268 0.8321862 0.03126641
## 30: 0.004779760 -1.4851268 0.8321862 0.03126641
## 31: 0.004779760 -1.4851268 0.8321862 0.03126641
## 32: 0.004779760 -1.4851268 0.8321862 0.03126641
## 33: 0.004779760 -1.4851268 0.8321862 0.03126641
## 34: 0.004779760 -1.4851268 0.8321862 0.03126641
## 35: 0.004779760 -1.4851268 0.8321862 0.03126641
## 36: 0.004779760 -1.4851268 0.8321862 0.03126641
## 37: 0.004779760 -1.4851268 0.8321862 0.03126641
## 38: 0.004779760 -1.4851268 0.8321862 0.03126641
## 39: 0.004779760 -1.4851268 0.8321862 0.03126641
## 40: 0.004779760 -1.4851268 0.8321862 0.03126641
## 41: 0.004779760 -1.4851268 0.8321862 0.03126641
## 42: 0.004779760 -1.4851268 0.8321862 0.03126641
## 43: 0.004779760 -1.4851268 0.8321862 0.03126641
## 44: 0.004779760 -1.4851268 0.8321862 0.03126641
## 45: 0.004779760 -1.4851268 0.8321862 0.03126641
## 46: 0.004779760 -1.4851268 0.8321862 0.03126641
## 47: 0.003860428 -2.3311288 1.1560091 0.25094155
## 48: 0.003860428 -2.3311288 1.1560091 0.25094155
## 49: 0.003860428 -2.3311288 1.1560091 0.25094155
## 50: 0.003860428 -2.3311288 1.1560091 0.25094155
## 51: 0.003860428 -2.3311288 1.1560091 0.25094155
## 52: 0.003860428 -2.3311288 1.1560091 0.25094155
## 53: 0.003860428 -2.3311288 1.1560091 0.25094155
## 54: 0.003860428 -2.3311288 1.1560091 0.25094155
## 55: 0.004540032 -1.5343905 0.7544213 0.01116250
## 56: 0.004540032 -1.5343905 0.7544213 0.01116250
## 57: 0.004540032 -1.5343905 0.7544213 0.01116250
## 58: 0.005075046 -0.7430393 0.3591568 0.52357949
## 59: 0.005075046 -0.7430393 0.3591568 0.52357949
## 60: 0.005075046 -0.7430393 0.3591568 0.52357949
## 61: 0.005075046 -0.7430393 0.3591568 0.52357949
## 62: 0.005075046 -0.7430393 0.3591568 0.52357949
## 63: 0.005075046 -0.7430393 0.3591568 0.52357949
## 64: 0.005075046 -0.7430393 0.3591568 0.52357949
## 65: 0.005075046 -0.7430393 0.3591568 0.52357949
## 66: 0.005075046 -0.7430393 0.3591568 0.52357949
## 67: 0.005075046 -0.7430393 0.3591568 0.52357949
## 68: 0.005075046 -0.7430393 0.3591568 0.52357949
## 69: 0.005075046 -0.7430393 0.3591568 0.52357949
## 70: 0.005075046 -0.7430393 0.3591568 0.52357949
## 71: 0.005372412 -1.2236534 1.2270317 0.25941579
## 72: 0.005372412 -1.2236534 1.2270317 0.25941579
## 73: 0.005372412 -1.2236534 1.2270317 0.25941579
## 74: 0.005372412 -1.2236534 1.2270317 0.25941579
## 75: 0.004342891 -2.0576952 1.1177425 0.48623810
## 76: 0.004342891 -2.0576952 1.1177425 0.48623810
##           se.bp          v         c       pchi

##  [1] "ORF61" "ORF21" "ORF49" "ORF19" "ORF31" "ORF1"  "ORF18" "ORF42" "ORF33"
## [10] "ORF62" "ORF69"
## [1] 11
##  [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF35" "ORF41" "ORF48" "ORF52" "ORF54"
## [10] "ORF57" "ORF60" "ORF71" "ORF72"
## [1] 13

Clustering statistics: Cluster number: 10

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  2:       1    ORF4 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  3:       1    ORF9 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  4:       1   ORF20 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  5:       1   ORF21 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  6:       1   ORF31 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  7:       1   ORF34 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  8:       1   ORF38 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  9:       1   ORF50 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 10:       1   ORF61 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 11:       1 ORF64_1 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 12:       2    ORF2 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 13:       2    ORF3 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 14:       2   ORF11 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 15:       2   ORF14 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 16:       2   ORF18 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 17:       2   ORF26 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 18:       2   ORF28 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 19:       2   ORF29 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 20:       2   ORF39 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 21:       2   ORF40 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 22:       2 ORF66_1 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 23:       2   ORF68 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 24:       2   ORF73 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 25:       2   ORF75 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 26:       2   ORF76 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 27:       3    ORF5 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 28:       3    ORF7 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 29:       3   ORF10 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 30:       3   ORF17 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 31:       3   ORF30 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 32:       3   ORF53 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 33:       3   ORF63 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 34:       3  NOIR_2 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 35:       4    ORF6 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 36:       4 ORF65_1 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 37:       4 ORF67_1 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 38:       5    ORF8 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 39:       5   ORF22 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 40:       5   ORF23 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 41:       5   ORF25 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 42:       5   ORF33 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 43:       5 ORF35.5 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 44:       5   ORF36 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 45:       5     CTO 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 46:       5   ORF42 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 47:       5   ORF43 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 48:       5   ORF44 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 49:       5   ORF46 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 50:       5   ORF58 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 51:       5   ORF62 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 52:       6   ORF12 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 53:       6   ORF13 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 54:       6   ORF15 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 55:       6   ORF16 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 56:       6   ORF35 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 57:       6   ORF41 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 58:       6   ORF48 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 59:       6   ORF52 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 60:       6   ORF54 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 61:       6   ORF57 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 62:       6   ORF60 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 63:       6   ORF71 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 64:       6   ORF72 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 65:       7   ORF19 0.9943260 0.9992519 0.8263791 0.0013907764 2.320885e-04
## 66:       7   ORF37 0.9943260 0.9992519 0.8263791 0.0013907764 2.320885e-04
## 67:       7   ORF49 0.9943260 0.9992519 0.8263791 0.0013907764 2.320885e-04
## 68:       7   ORF51 0.9943260 0.9992519 0.8263791 0.0013907764 2.320885e-04
## 69:       8   ORF24 0.8068307 0.9518750 0.6212922 0.0225487111 7.848995e-03
## 70:       8   ORF74 0.8068307 0.9518750 0.6212922 0.0225487111 7.848995e-03
## 71:       9   ORF27 0.3899144 0.8542940 0.3575105 0.0474166185 1.852864e-02
## 72:       9   ORF32 0.3899144 0.8542940 0.3575105 0.0474166185 1.852864e-02
## 73:       9   ORF59 0.3899144 0.8542940 0.3575105 0.0474166185 1.852864e-02
## 74:       9  NOIR_1 0.3899144 0.8542940 0.3575105 0.0474166185 1.852864e-02
## 75:      10   ORF69 0.9895706 0.9986972 0.7609269 0.0022493614 3.637036e-04
## 76:      10   ORF70 0.9895706 0.9986972 0.7609269 0.0022493614 3.637036e-04
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.002430598 -2.7030290 0.9688488 0.39059013
##  2: 0.002430598 -2.7030290 0.9688488 0.39059013
##  3: 0.002430598 -2.7030290 0.9688488 0.39059013
##  4: 0.002430598 -2.7030290 0.9688488 0.39059013
##  5: 0.002430598 -2.7030290 0.9688488 0.39059013
##  6: 0.002430598 -2.7030290 0.9688488 0.39059013
##  7: 0.002430598 -2.7030290 0.9688488 0.39059013
##  8: 0.002430598 -2.7030290 0.9688488 0.39059013
##  9: 0.002430598 -2.7030290 0.9688488 0.39059013
## 10: 0.002430598 -2.7030290 0.9688488 0.39059013
## 11: 0.002430598 -2.7030290 0.9688488 0.39059013
## 12: 0.004779760 -1.4851268 0.8321862 0.03126641
## 13: 0.004779760 -1.4851268 0.8321862 0.03126641
## 14: 0.004779760 -1.4851268 0.8321862 0.03126641
## 15: 0.004779760 -1.4851268 0.8321862 0.03126641
## 16: 0.004779760 -1.4851268 0.8321862 0.03126641
## 17: 0.004779760 -1.4851268 0.8321862 0.03126641
## 18: 0.004779760 -1.4851268 0.8321862 0.03126641
## 19: 0.004779760 -1.4851268 0.8321862 0.03126641
## 20: 0.004779760 -1.4851268 0.8321862 0.03126641
## 21: 0.004779760 -1.4851268 0.8321862 0.03126641
## 22: 0.004779760 -1.4851268 0.8321862 0.03126641
## 23: 0.004779760 -1.4851268 0.8321862 0.03126641
## 24: 0.004779760 -1.4851268 0.8321862 0.03126641
## 25: 0.004779760 -1.4851268 0.8321862 0.03126641
## 26: 0.004779760 -1.4851268 0.8321862 0.03126641
## 27: 0.003860428 -2.3311288 1.1560091 0.25094155
## 28: 0.003860428 -2.3311288 1.1560091 0.25094155
## 29: 0.003860428 -2.3311288 1.1560091 0.25094155
## 30: 0.003860428 -2.3311288 1.1560091 0.25094155
## 31: 0.003860428 -2.3311288 1.1560091 0.25094155
## 32: 0.003860428 -2.3311288 1.1560091 0.25094155
## 33: 0.003860428 -2.3311288 1.1560091 0.25094155
## 34: 0.003860428 -2.3311288 1.1560091 0.25094155
## 35: 0.004540032 -1.5343905 0.7544213 0.01116250
## 36: 0.004540032 -1.5343905 0.7544213 0.01116250
## 37: 0.004540032 -1.5343905 0.7544213 0.01116250
## 38: 0.005075046 -0.7430393 0.3591568 0.52357949
## 39: 0.005075046 -0.7430393 0.3591568 0.52357949
## 40: 0.005075046 -0.7430393 0.3591568 0.52357949
## 41: 0.005075046 -0.7430393 0.3591568 0.52357949
## 42: 0.005075046 -0.7430393 0.3591568 0.52357949
## 43: 0.005075046 -0.7430393 0.3591568 0.52357949
## 44: 0.005075046 -0.7430393 0.3591568 0.52357949
## 45: 0.005075046 -0.7430393 0.3591568 0.52357949
## 46: 0.005075046 -0.7430393 0.3591568 0.52357949
## 47: 0.005075046 -0.7430393 0.3591568 0.52357949
## 48: 0.005075046 -0.7430393 0.3591568 0.52357949
## 49: 0.005075046 -0.7430393 0.3591568 0.52357949
## 50: 0.005075046 -0.7430393 0.3591568 0.52357949
## 51: 0.005075046 -0.7430393 0.3591568 0.52357949
## 52: 0.005372412 -1.2236534 1.2270317 0.25941579
## 53: 0.005372412 -1.2236534 1.2270317 0.25941579
## 54: 0.005372412 -1.2236534 1.2270317 0.25941579
## 55: 0.005372412 -1.2236534 1.2270317 0.25941579
## 56: 0.005372412 -1.2236534 1.2270317 0.25941579
## 57: 0.005372412 -1.2236534 1.2270317 0.25941579
## 58: 0.005372412 -1.2236534 1.2270317 0.25941579
## 59: 0.005372412 -1.2236534 1.2270317 0.25941579
## 60: 0.005372412 -1.2236534 1.2270317 0.25941579
## 61: 0.005372412 -1.2236534 1.2270317 0.25941579
## 62: 0.005372412 -1.2236534 1.2270317 0.25941579
## 63: 0.005372412 -1.2236534 1.2270317 0.25941579
## 64: 0.005372412 -1.2236534 1.2270317 0.25941579
## 65: 0.004342891 -2.0576952 1.1177425 0.48623810
## 66: 0.004342891 -2.0576952 1.1177425 0.48623810
## 67: 0.004342891 -2.0576952 1.1177425 0.48623810
## 68: 0.004342891 -2.0576952 1.1177425 0.48623810
## 69: 0.005188565 -0.9860940 0.6772176 0.02169720
## 70: 0.005188565 -0.9860940 0.6772176 0.02169720
## 71: 0.005045718 -0.3449540 0.7100752 0.02701528
## 72: 0.005045718 -0.3449540 0.7100752 0.02701528
## 73: 0.005045718 -0.3449540 0.7100752 0.02701528
## 74: 0.005045718 -0.3449540 0.7100752 0.02701528
## 75: 0.004764688 -1.8600434 1.1507559 0.01367498
## 76: 0.004764688 -1.8600434 1.1507559 0.01367498
##           se.bp          v         c       pchi

## [1] "ORF1"  "ORF68" "ORF36" "ORF19" "ORF49" "ORF59" "ORF69"
## [1] 7
##  [1] "ORF8"    "ORF22"   "ORF23"   "ORF25"   "ORF33"   "ORF35.5" "ORF36"  
##  [8] "CTO"     "ORF42"   "ORF43"   "ORF44"   "ORF46"   "ORF58"   "ORF62"  
## [15] "ORF27"   "ORF32"   "ORF59"   "NOIR_1"
## [1] 18

Clustering statistics: Cluster number: 12

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  2:       1    ORF4 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  3:       1    ORF9 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  4:       1   ORF20 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  5:       1   ORF21 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  6:       1   ORF31 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  7:       1   ORF34 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  8:       1   ORF38 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  9:       1   ORF50 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 10:       1   ORF61 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 11:       2    ORF2 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 12:       2    ORF3 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 13:       2   ORF11 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 14:       2   ORF14 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 15:       2   ORF18 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 16:       2   ORF26 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 17:       2   ORF28 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 18:       2   ORF29 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 19:       2   ORF39 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 20:       2   ORF40 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 21:       2 ORF66_1 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 22:       2   ORF68 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 23:       2   ORF73 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 24:       2   ORF75 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 25:       2   ORF76 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 26:       3    ORF5 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 27:       3    ORF7 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 28:       3   ORF10 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 29:       3   ORF17 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 30:       3   ORF30 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 31:       3   ORF53 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 32:       3   ORF63 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 33:       3  NOIR_2 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 34:       4    ORF6 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 35:       4 ORF65_1 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 36:       4 ORF67_1 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 37:       5    ORF8 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 38:       5   ORF22 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 39:       5   ORF23 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 40:       5   ORF25 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 41:       5   ORF33 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 42:       5 ORF35.5 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 43:       5   ORF36 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 44:       5     CTO 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 45:       5   ORF42 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 46:       5   ORF43 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 47:       5   ORF44 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 48:       5   ORF46 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 49:       5   ORF58 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 50:       5   ORF62 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 51:       6   ORF12 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 52:       6   ORF13 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 53:       6   ORF15 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 54:       6   ORF16 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 55:       6   ORF35 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 56:       6   ORF41 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 57:       6   ORF48 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 58:       6   ORF52 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 59:       6   ORF54 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 60:       6   ORF57 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 61:       6   ORF60 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 62:       6   ORF71 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 63:       6   ORF72 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 64:       7   ORF19 0.9943260 0.9992519 0.8263791 0.0013907764 2.320885e-04
## 65:       7   ORF37 0.9943260 0.9992519 0.8263791 0.0013907764 2.320885e-04
## 66:       7   ORF49 0.9943260 0.9992519 0.8263791 0.0013907764 2.320885e-04
## 67:       7   ORF51 0.9943260 0.9992519 0.8263791 0.0013907764 2.320885e-04
## 68:       8   ORF24 0.8068307 0.9518750 0.6212922 0.0225487111 7.848995e-03
## 69:       8   ORF74 0.8068307 0.9518750 0.6212922 0.0225487111 7.848995e-03
## 70:       9   ORF27 0.3899144 0.8542940 0.3575105 0.0474166185 1.852864e-02
## 71:       9   ORF32 0.3899144 0.8542940 0.3575105 0.0474166185 1.852864e-02
## 72:       9   ORF59 0.3899144 0.8542940 0.3575105 0.0474166185 1.852864e-02
## 73:      10 ORF64_1 0.9895706 0.9986972 0.7609269 0.0022493614 3.637036e-04
## 74:      11  NOIR_1 0.9891288 0.9983648 0.8083363 0.0024065917 4.618993e-04
## 75:      12   ORF69 0.5421251 0.9301339 0.2829816 0.0475015862 1.176034e-02
## 76:      12   ORF70 0.5421251 0.9301339 0.2829816 0.0475015862 1.176034e-02
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.002430598 -2.7030290 0.9688488 0.39059013
##  2: 0.002430598 -2.7030290 0.9688488 0.39059013
##  3: 0.002430598 -2.7030290 0.9688488 0.39059013
##  4: 0.002430598 -2.7030290 0.9688488 0.39059013
##  5: 0.002430598 -2.7030290 0.9688488 0.39059013
##  6: 0.002430598 -2.7030290 0.9688488 0.39059013
##  7: 0.002430598 -2.7030290 0.9688488 0.39059013
##  8: 0.002430598 -2.7030290 0.9688488 0.39059013
##  9: 0.002430598 -2.7030290 0.9688488 0.39059013
## 10: 0.002430598 -2.7030290 0.9688488 0.39059013
## 11: 0.004779760 -1.4851268 0.8321862 0.03126641
## 12: 0.004779760 -1.4851268 0.8321862 0.03126641
## 13: 0.004779760 -1.4851268 0.8321862 0.03126641
## 14: 0.004779760 -1.4851268 0.8321862 0.03126641
## 15: 0.004779760 -1.4851268 0.8321862 0.03126641
## 16: 0.004779760 -1.4851268 0.8321862 0.03126641
## 17: 0.004779760 -1.4851268 0.8321862 0.03126641
## 18: 0.004779760 -1.4851268 0.8321862 0.03126641
## 19: 0.004779760 -1.4851268 0.8321862 0.03126641
## 20: 0.004779760 -1.4851268 0.8321862 0.03126641
## 21: 0.004779760 -1.4851268 0.8321862 0.03126641
## 22: 0.004779760 -1.4851268 0.8321862 0.03126641
## 23: 0.004779760 -1.4851268 0.8321862 0.03126641
## 24: 0.004779760 -1.4851268 0.8321862 0.03126641
## 25: 0.004779760 -1.4851268 0.8321862 0.03126641
## 26: 0.003860428 -2.3311288 1.1560091 0.25094155
## 27: 0.003860428 -2.3311288 1.1560091 0.25094155
## 28: 0.003860428 -2.3311288 1.1560091 0.25094155
## 29: 0.003860428 -2.3311288 1.1560091 0.25094155
## 30: 0.003860428 -2.3311288 1.1560091 0.25094155
## 31: 0.003860428 -2.3311288 1.1560091 0.25094155
## 32: 0.003860428 -2.3311288 1.1560091 0.25094155
## 33: 0.003860428 -2.3311288 1.1560091 0.25094155
## 34: 0.004540032 -1.5343905 0.7544213 0.01116250
## 35: 0.004540032 -1.5343905 0.7544213 0.01116250
## 36: 0.004540032 -1.5343905 0.7544213 0.01116250
## 37: 0.005075046 -0.7430393 0.3591568 0.52357949
## 38: 0.005075046 -0.7430393 0.3591568 0.52357949
## 39: 0.005075046 -0.7430393 0.3591568 0.52357949
## 40: 0.005075046 -0.7430393 0.3591568 0.52357949
## 41: 0.005075046 -0.7430393 0.3591568 0.52357949
## 42: 0.005075046 -0.7430393 0.3591568 0.52357949
## 43: 0.005075046 -0.7430393 0.3591568 0.52357949
## 44: 0.005075046 -0.7430393 0.3591568 0.52357949
## 45: 0.005075046 -0.7430393 0.3591568 0.52357949
## 46: 0.005075046 -0.7430393 0.3591568 0.52357949
## 47: 0.005075046 -0.7430393 0.3591568 0.52357949
## 48: 0.005075046 -0.7430393 0.3591568 0.52357949
## 49: 0.005075046 -0.7430393 0.3591568 0.52357949
## 50: 0.005075046 -0.7430393 0.3591568 0.52357949
## 51: 0.005372412 -1.2236534 1.2270317 0.25941579
## 52: 0.005372412 -1.2236534 1.2270317 0.25941579
## 53: 0.005372412 -1.2236534 1.2270317 0.25941579
## 54: 0.005372412 -1.2236534 1.2270317 0.25941579
## 55: 0.005372412 -1.2236534 1.2270317 0.25941579
## 56: 0.005372412 -1.2236534 1.2270317 0.25941579
## 57: 0.005372412 -1.2236534 1.2270317 0.25941579
## 58: 0.005372412 -1.2236534 1.2270317 0.25941579
## 59: 0.005372412 -1.2236534 1.2270317 0.25941579
## 60: 0.005372412 -1.2236534 1.2270317 0.25941579
## 61: 0.005372412 -1.2236534 1.2270317 0.25941579
## 62: 0.005372412 -1.2236534 1.2270317 0.25941579
## 63: 0.005372412 -1.2236534 1.2270317 0.25941579
## 64: 0.004342891 -2.0576952 1.1177425 0.48623810
## 65: 0.004342891 -2.0576952 1.1177425 0.48623810
## 66: 0.004342891 -2.0576952 1.1177425 0.48623810
## 67: 0.004342891 -2.0576952 1.1177425 0.48623810
## 68: 0.005188565 -0.9860940 0.6772176 0.02169720
## 69: 0.005188565 -0.9860940 0.6772176 0.02169720
## 70: 0.005045718 -0.3449540 0.7100752 0.02701528
## 71: 0.005045718 -0.3449540 0.7100752 0.02701528
## 72: 0.005045718 -0.3449540 0.7100752 0.02701528
## 73: 0.004764688 -1.8600434 1.1507559 0.01367498
## 74: 0.004443932 -1.9064492 1.0346673 0.61787513
## 75: 0.004732731 -0.4513912 1.0253980 0.29575721
## 76: 0.004732731 -0.4513912 1.0253980 0.29575721
##           se.bp          v         c       pchi

## [1] "ORF68" "ORF36" "ORF19" "ORF49" "ORF69"
## [1] 5
##  [1] "ORF8"    "ORF22"   "ORF23"   "ORF25"   "ORF33"   "ORF35.5" "ORF36"  
##  [8] "CTO"     "ORF42"   "ORF43"   "ORF44"   "ORF46"   "ORF58"   "ORF62"  
## [15] "ORF27"   "ORF32"   "ORF59"   "ORF69"   "ORF70"
## [1] 19

Selected number of clusters: 12

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  2:       1    ORF4 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  3:       1    ORF9 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  4:       1   ORF20 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  5:       1   ORF21 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  6:       1   ORF31 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  7:       1   ORF34 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  8:       1   ORF38 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
##  9:       1   ORF50 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 10:       1   ORF61 0.9992761 0.9998796 0.9585569 0.0002977028 5.897464e-05
## 11:       2    ORF2 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 12:       2    ORF3 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 13:       2   ORF11 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 14:       2   ORF14 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 15:       2   ORF18 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 16:       2   ORF26 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 17:       2   ORF28 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 18:       2   ORF29 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 19:       2   ORF39 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 20:       2   ORF40 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 21:       2 ORF66_1 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 22:       2   ORF68 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 23:       2   ORF73 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 24:       2   ORF75 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 25:       2   ORF76 0.9494535 0.9897567 0.7431027 0.0084008353 2.239149e-03
## 26:       3    ORF5 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 27:       3    ORF7 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 28:       3   ORF10 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 29:       3   ORF17 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 30:       3   ORF30 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 31:       3   ORF53 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 32:       3   ORF63 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 33:       3  NOIR_2 0.9980288 0.9997559 0.8800266 0.0005862713 8.999375e-05
## 34:       4    ORF6 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 35:       4 ORF65_1 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 36:       4 ORF67_1 0.9509754 0.9889549 0.7822955 0.0083504459 2.443599e-03
## 37:       5    ORF8 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 38:       5   ORF22 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 39:       5   ORF23 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 40:       5   ORF25 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 41:       5   ORF33 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 42:       5 ORF35.5 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 43:       5   ORF36 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 44:       5     CTO 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 45:       5   ORF42 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 46:       5   ORF43 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 47:       5   ORF44 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 48:       5   ORF46 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 49:       5   ORF58 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 50:       5   ORF62 0.6242046 0.8648118 0.6494672 0.0330366420 1.696974e-02
## 51:       6   ORF12 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 52:       6   ORF13 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 53:       6   ORF15 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 54:       6   ORF16 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 55:       6   ORF35 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 56:       6   ORF41 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 57:       6   ORF48 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 58:       6   ORF52 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 59:       6   ORF54 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 60:       6   ORF57 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 61:       6   ORF60 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 62:       6   ORF71 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 63:       6   ORF72 0.9351330 0.9928708 0.4986523 0.0104582015 1.619060e-03
## 64:       7   ORF19 0.9943260 0.9992519 0.8263791 0.0013907764 2.320885e-04
## 65:       7   ORF37 0.9943260 0.9992519 0.8263791 0.0013907764 2.320885e-04
## 66:       7   ORF49 0.9943260 0.9992519 0.8263791 0.0013907764 2.320885e-04
## 67:       7   ORF51 0.9943260 0.9992519 0.8263791 0.0013907764 2.320885e-04
## 68:       8   ORF24 0.8068307 0.9518750 0.6212922 0.0225487111 7.848995e-03
## 69:       8   ORF74 0.8068307 0.9518750 0.6212922 0.0225487111 7.848995e-03
## 70:       9   ORF27 0.3899144 0.8542940 0.3575105 0.0474166185 1.852864e-02
## 71:       9   ORF32 0.3899144 0.8542940 0.3575105 0.0474166185 1.852864e-02
## 72:       9   ORF59 0.3899144 0.8542940 0.3575105 0.0474166185 1.852864e-02
## 73:      10 ORF64_1 0.9895706 0.9986972 0.7609269 0.0022493614 3.637036e-04
## 74:      11  NOIR_1 0.9891288 0.9983648 0.8083363 0.0024065917 4.618993e-04
## 75:      12   ORF69 0.5421251 0.9301339 0.2829816 0.0475015862 1.176034e-02
## 76:      12   ORF70 0.5421251 0.9301339 0.2829816 0.0475015862 1.176034e-02
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.002430598 -2.7030290 0.9688488 0.39059013
##  2: 0.002430598 -2.7030290 0.9688488 0.39059013
##  3: 0.002430598 -2.7030290 0.9688488 0.39059013
##  4: 0.002430598 -2.7030290 0.9688488 0.39059013
##  5: 0.002430598 -2.7030290 0.9688488 0.39059013
##  6: 0.002430598 -2.7030290 0.9688488 0.39059013
##  7: 0.002430598 -2.7030290 0.9688488 0.39059013
##  8: 0.002430598 -2.7030290 0.9688488 0.39059013
##  9: 0.002430598 -2.7030290 0.9688488 0.39059013
## 10: 0.002430598 -2.7030290 0.9688488 0.39059013
## 11: 0.004779760 -1.4851268 0.8321862 0.03126641
## 12: 0.004779760 -1.4851268 0.8321862 0.03126641
## 13: 0.004779760 -1.4851268 0.8321862 0.03126641
## 14: 0.004779760 -1.4851268 0.8321862 0.03126641
## 15: 0.004779760 -1.4851268 0.8321862 0.03126641
## 16: 0.004779760 -1.4851268 0.8321862 0.03126641
## 17: 0.004779760 -1.4851268 0.8321862 0.03126641
## 18: 0.004779760 -1.4851268 0.8321862 0.03126641
## 19: 0.004779760 -1.4851268 0.8321862 0.03126641
## 20: 0.004779760 -1.4851268 0.8321862 0.03126641
## 21: 0.004779760 -1.4851268 0.8321862 0.03126641
## 22: 0.004779760 -1.4851268 0.8321862 0.03126641
## 23: 0.004779760 -1.4851268 0.8321862 0.03126641
## 24: 0.004779760 -1.4851268 0.8321862 0.03126641
## 25: 0.004779760 -1.4851268 0.8321862 0.03126641
## 26: 0.003860428 -2.3311288 1.1560091 0.25094155
## 27: 0.003860428 -2.3311288 1.1560091 0.25094155
## 28: 0.003860428 -2.3311288 1.1560091 0.25094155
## 29: 0.003860428 -2.3311288 1.1560091 0.25094155
## 30: 0.003860428 -2.3311288 1.1560091 0.25094155
## 31: 0.003860428 -2.3311288 1.1560091 0.25094155
## 32: 0.003860428 -2.3311288 1.1560091 0.25094155
## 33: 0.003860428 -2.3311288 1.1560091 0.25094155
## 34: 0.004540032 -1.5343905 0.7544213 0.01116250
## 35: 0.004540032 -1.5343905 0.7544213 0.01116250
## 36: 0.004540032 -1.5343905 0.7544213 0.01116250
## 37: 0.005075046 -0.7430393 0.3591568 0.52357949
## 38: 0.005075046 -0.7430393 0.3591568 0.52357949
## 39: 0.005075046 -0.7430393 0.3591568 0.52357949
## 40: 0.005075046 -0.7430393 0.3591568 0.52357949
## 41: 0.005075046 -0.7430393 0.3591568 0.52357949
## 42: 0.005075046 -0.7430393 0.3591568 0.52357949
## 43: 0.005075046 -0.7430393 0.3591568 0.52357949
## 44: 0.005075046 -0.7430393 0.3591568 0.52357949
## 45: 0.005075046 -0.7430393 0.3591568 0.52357949
## 46: 0.005075046 -0.7430393 0.3591568 0.52357949
## 47: 0.005075046 -0.7430393 0.3591568 0.52357949
## 48: 0.005075046 -0.7430393 0.3591568 0.52357949
## 49: 0.005075046 -0.7430393 0.3591568 0.52357949
## 50: 0.005075046 -0.7430393 0.3591568 0.52357949
## 51: 0.005372412 -1.2236534 1.2270317 0.25941579
## 52: 0.005372412 -1.2236534 1.2270317 0.25941579
## 53: 0.005372412 -1.2236534 1.2270317 0.25941579
## 54: 0.005372412 -1.2236534 1.2270317 0.25941579
## 55: 0.005372412 -1.2236534 1.2270317 0.25941579
## 56: 0.005372412 -1.2236534 1.2270317 0.25941579
## 57: 0.005372412 -1.2236534 1.2270317 0.25941579
## 58: 0.005372412 -1.2236534 1.2270317 0.25941579
## 59: 0.005372412 -1.2236534 1.2270317 0.25941579
## 60: 0.005372412 -1.2236534 1.2270317 0.25941579
## 61: 0.005372412 -1.2236534 1.2270317 0.25941579
## 62: 0.005372412 -1.2236534 1.2270317 0.25941579
## 63: 0.005372412 -1.2236534 1.2270317 0.25941579
## 64: 0.004342891 -2.0576952 1.1177425 0.48623810
## 65: 0.004342891 -2.0576952 1.1177425 0.48623810
## 66: 0.004342891 -2.0576952 1.1177425 0.48623810
## 67: 0.004342891 -2.0576952 1.1177425 0.48623810
## 68: 0.005188565 -0.9860940 0.6772176 0.02169720
## 69: 0.005188565 -0.9860940 0.6772176 0.02169720
## 70: 0.005045718 -0.3449540 0.7100752 0.02701528
## 71: 0.005045718 -0.3449540 0.7100752 0.02701528
## 72: 0.005045718 -0.3449540 0.7100752 0.02701528
## 73: 0.004764688 -1.8600434 1.1507559 0.01367498
## 74: 0.004443932 -1.9064492 1.0346673 0.61787513
## 75: 0.004732731 -0.4513912 1.0253980 0.29575721
## 76: 0.004732731 -0.4513912 1.0253980 0.29575721
##           se.bp          v         c       pchi

## [1] "ORF68" "ORF36" "ORF19" "ORF49" "ORF69"
## [1] 5
##  [1] "ORF8"    "ORF22"   "ORF23"   "ORF25"   "ORF33"   "ORF35.5" "ORF36"  
##  [8] "CTO"     "ORF42"   "ORF43"   "ORF44"   "ORF46"   "ORF58"   "ORF62"  
## [15] "ORF27"   "ORF32"   "ORF59"   "ORF69"   "ORF70"
## [1] 19

Remove genes from clusters ?

##  [1] "ORF8"    "ORF22"   "ORF23"   "ORF25"   "ORF33"   "ORF35.5" "ORF36"  
##  [8] "CTO"     "ORF42"   "ORF43"   "ORF44"   "ORF46"   "ORF58"   "ORF62"  
## [15] "ORF27"   "ORF32"   "ORF59"   "ORF69"   "ORF70"
## [1] 19
## No genes were removed from their corresponding clusters.
##     cluster     N
##       <int> <int>
##  1:       2    15
##  2:       5    14
##  3:       6    13
##  4:       1    10
##  5:       3     8
##  6:       7     4
##  7:       4     3
##  8:       9     3
##  9:       8     2
## 10:      12     2
## 11:      10     1
## 12:      11     1

Merge cluster stats

Assigning genes to clusters

Summarize and melt

Heatmaps

Normalized Expression

Expression delta ~ 6 hpi

Z-score of expression delta ~ 6 hpi

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 4 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Compare literature and de novo kinetic classes

NA shows the number of genes where the clustering did not yield an unambiguous result.

Combined Kinetic classes

De Novo Clusters

Literature clusters